Biology subjects

Ribeiro, D.

Publications and source records attributed to Ribeiro, D..

16 recordsLinked to original sources

bioRxiv2026

Host tRNA modifications drive efficient translation of influenza A virus genome and impact host antiviral stress responses

Influenza A virus (IAV), as all other viruses, is completely dependent on the host translation machinery components, including host transfer RNAs (tRNAs), to effectively decode its genome. However, while the human genome is biased towards cytosine (C) and guanosine (G)-ending codons, the IAV genome is skewed towards adenine (A) and uridine (U)-ending codons. Nevertheless, translation of IAVs RNA genome is highly efficient. Here we show that host tRNA and tRNA epitranscriptome dynamics are important regulators of IAV RNA translation and host antiviral responses. We show that the levels of several tRNA modifications, including 5-methylcarboxymethyluridine (mcm5U34) and 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), and their cognate writers, vary over the course of IAV infection. Additionally, we demonstrate that a set of tRNAs are preferentially recruited to ribosomes upon IAV infection, in line with IAV codon usage requirements. We further show that loss of ELP3, the catalytic subunit of the elongator complex, which is involved in the catalysis of mcm5U34 and of mcm5s2U34, induces tRNA hypomodifications, impairs translation of codon biased IAV genes and triggers the integrated stress response (ISR), interfering with IAV propagation. Taken together, our results uncover the relevance of host tRNAs and their modifications for optimal expression of viral genomes and host antiviral responses, setting the tRNA epitranscriptome as a promising target for the development of host-based antiviral therapies.

molecular biology↗

bioRxiv2026

Selective profiling of translationally active tRNAs and their dynamics under stress

During translation, transfer RNAs (tRNAs) deliver specific amino acids to the ribosome in a coordinated manner with the sequence encoded by the mRNA. Despite their central role in protein synthesis, their precise contribution to the modulation of translation remains poorly understood, primarily due to lack of methods to characterise tRNA abundances and their modifications from actively translating ribosomes. Here we develop tRIBO-seq, a simple and robust nanopore-based method to selectively capture ribosome-associated native tRNA populations (ribo-tRNAs) from actively translating ribosomes, providing tRNA abundance, modification and fragmentation information from a single experiment. Using tRIBO-seq, we find that ribo-tRNAs, but often not total tRNAs, are significantly altered upon stress. Notably, we find that tRNAome alterations strongly vary depending on the stress type: while viral infection and leucine deprivation leads to changes in ribo-tRNA abundances, methionine starvation causes a dramatic loss of methyl-based tRNA modifications. By contrast, we find that arsenite exposure does not alter tRNA abundances nor modification patterns, but rather causes major fragmentation events in selected subsets of ribo-tRNAs. Altogether, tRIBO-seq offers a robust and reproducible approach to map the full tRNA landscape -capturing tRNA abundance, modification and fragmentation patterns-, across both total and actively translating tRNA populations, revealing the dynamics of the tRNAome with unprecedented resolution, in a single experiment.

molecular biology↗

bioRxiv2025

Characterizing Compounds Targeting Colorectal Cancer Derived From Monastrol Using High-Through Screening of an Extensive Combinatorial Library

BackgroundCancer remains a critical global health concern. Among its various forms, colorectal cancer (CRC) stands out due to its high prevalence and mortality rates, emphasizing the urgent need for novel therapeutic agents to enhance treatment efficacy and prolong patient survival. Monastrol, an antimitotic compound known to bind kinesin Eg5, is employed in some cancer therapies. Recent studies have revealed that monastrol also interacts with fascin, a protein implicated in tumor aggressiveness and metastasis, thereby disrupting microtubule dynamics and actin bundling, ultimately impairing cell migration. MethodsIn this work, we developed a workflow to identify fascin-binding compounds based on a monastrol-derived pharmacophore model, integrating in silico predictions with in vitro validation. We performed ligand-based virtual screening using a pharmacophore model constructed from monastrol, applied to a high-throughput screening (HTS) library of 1.6 million compounds. The top-ranking candidates from the virtual screening were subsequently subjected to physicochemical characterization and cellular assays. ResultsTwo compounds (designated Z118298144 and Z17544625) were identified that exhibited strong binding to fascin and inhibited actin bundling in physicochemical assays. Furthermore, cellular experiments demonstrated that both compounds reduced proliferation and impaired migration of CRC cells at micromolar concentrations. ConclusionsWe established an optimized pipeline combining virtual screening with experimental validation to efficiently identify fascin inhibitors. Using this approach, we discovered two promising compounds with anticancer activity in CRC cell cultures. Moreover, the protocol has been successfully adapted for application to additional cancer-related targets, expanding its potential utility in drug discovery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/667829v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@dc470eorg.highwire.dtl.DTLVardef@1bd0759org.highwire.dtl.DTLVardef@12d755dorg.highwire.dtl.DTLVardef@1742d45_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, implementation of eDNA as a standard protocol in long-term monitoring programs, that have traditionally relied on capture-based methods, poses challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For most species or species-groups analyzed individually (13 out of 17), there was a significant correspondence between electrofishing and eDNA metabarcoding detections. The correspondence was weaker when comparing the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

ecology↗

bioRxiv2024

Discovery of Z1362873773: A Novel Fascin Inhibitor from a Large Chemical Library for Colorectal Cancer

Metastasis is one of the leading causes of cancer-related death worldwide. Fascin is involved in this process by bundling actin filaments and producing protrusions in cancer cells, which facilitate their migration. It has been shown that the overexpression of this protein is related to the appearance of different types of cancer, such as colorectal cancer. In this study, we conducted an in silico screening against the enamine library, a compound library with a broad chemical space ({approx}1.4M compounds), followed by further validation with physicochemical assays and cellular migration and cytotoxicity tests, thereby obtaining a molecule with considerable fascin inhibitory and migration-arresting capacity similar to other inhibitors already known in the literature. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/606007v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@10ddb2borg.highwire.dtl.DTLVardef@afe8b1org.highwire.dtl.DTLVardef@d5f436org.highwire.dtl.DTLVardef@940ddc_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Neuron Derived Cytokine Interleukin-34 Controls Developmental Microglia Function

Neuron-microglia interactions dictate the development of neuronal circuits in the brain. However, the factors that regulate these processes across development are largely unknown. Here, we find that IL34, a neuron-derived cytokine, is upregulated in early development and maintains neuroprotective, mature microglia in the anterior cingulate cortex (ACC) of mice. We show that IL34 is upregulated in the second week of postnatal life and is expressed primarily in excitatory neurons. Excitatory-neuron specific knock-out of IL34 reduced microglia number and TMEM119 expression and increased aberrant microglial phagocytosis of excitatory thalamocortical synapses in the ACC. Acute, low dose blocking of IL34 at postnatal day 15 similarly decreased TMEM119 and inappropriately increased microglial phagocytosis of synapses. Viral overexpression of IL34 induced TMEM119 expression and prevented appropriate microglial phagocytosis of synapses. These findings establish IL34 as a key regulator of neuron-microglia crosstalk in postnatal brain development, controlling both microglial maturation and synapse engulfment.

neuroscience↗

bioRxiv2024

Deep Learning Outperforms Classical Machine Learning Methods in Pediatric Brain Tumor Classification through Mass Spectra

Pediatric brain tumors are the most common cause of death among all childhood cancers and surgical resection usually is the first step in disease management. During surgery, it is important to perform safe gross resection of tumors, retaining as much brain tissue as possible. Therefore, appropriate resection margin delineation is extremely relevant. Currently available methods for tissue analysis have limited precision, are time-consuming, and often require multiple invasive procedures. Our main goal is to test whether machine learning techniques are capable of classifying the pediatric brain tissue chemical profile generated by DESI-MSI, which is mainly lipidic, into normal or abnormal tissue and into low- and high-grade malignancy subareas within each sample. Our experiments show that deep learning methods outperform classical machine learning methods in the task of classifying brain tissue from DESI-MSI mass spectra, both in normal versus abnormal tissue, and, for malignant tissues, in low-grade versus high-grade malignancy. Our conclusion are based on the analysis of 34,870 annotated spectra, obtained from the neoplastic and non-neoplastic microanatomical stratification of individual samples from 116 pediatric patients who underwent brain tumor surgical resection at the Boldrini Childrens Center between 2000 and 2020. Support Vector Machines, Random, Forests, and Least Absolute Shrinkage and Selection Operator (LASSO) were among the classical machine learning techniques evaluated.

bioinformatics↗

bioRxiv2023

Non-coding rare variant associations with blood traits on 166,740 UK Biobank genomes

Large biobanks with whole-genome sequencing now enable the association of non-coding rare variants with complex human traits. Given that >98% of the genome is available for exploration, the selection of non-coding variants remains a critical yet unresolved challenge in these analyses. Here, we leverage knowledge of blood gene regulation and deleteriousness scores to select non-coding variants pertinent for association with blood-related traits. We leverage whole genome sequencing and 59 blood cell count and biomarker measurements for 166 740 UK Biobank samples to perform variant collapsing tests. We identified hundreds of gene-trait associations involving non-coding variants across the 59 traits. However, we demonstrate that the majority of these non-coding rare variant associations (i) reproduce associations known from common variant studies and (ii) are driven by linkage disequilibrium between nearby common and rare variants. This study underscores the prevailing challenges in rare variant analysis and the need for caution when interpreting non-coding rare variant association results.

genetics↗

bioRxiv2023

Reproductive traits of the European catfish (Silurus glanis) during the early stages of invasion in the Lower Tagus River

Freshwater ecosystems face severe challenges from biological invasions, leading to biodiversity loss, disruption of ecosystem services, and economic impacts. Human-mediated activities, such as aquarium trade and sport angling, contribute to species introductions, with potential negative consequences for native ecosystems. The European catfish (Silurus glanis) is one of the worlds largest freshwater fish and has been intentionally introduced into diverse regions, impacting native ecosystems. However, limited research exists on its reproductive traits outside its native range. This study addresses this gap by examining the reproductive characteristics of non-native European catfish populations in the Lower Tagus River in Portugal, focusing on size at maturity, spawning period, and fecundity. The observed balanced sex ratio aligns with studies of native populations. Variations in size at first maturity (TL50) among populations highlight the influence of habitat conditions, temperature, food availability, growth rate, and geographical location on this trait. The extended spawning season (March to June) in the Tagus River is consistent with native populations, but variations may occur based on environmental conditions and water temperature. Absolute fecundity ranged from 8,961 to 335,500 oocytes, showing positive relationships with body size and emphasizing the reproductive potential of European catfish in Portugal. Egg size variations, along with asynchronous egg development, contribute to the species reproductive strategy, favoring its invasive success. Management efforts should include monitoring, regulations on introductions, removal programs, and public awareness to mitigate their impact. Future research should focus on understanding how non-native European catfish populations adapt in various regions and continue to impact ecosystems.

ecology↗

bioRxiv2023

Influenza A virus activates the unfolded protein response and induces the accumulation of insoluble protein aggregates that are essential for efficient viral propagation

Influenza A virus (IAV) is one of the main causes of annual respiratory epidemics in humans. IAV employs multiple strategies to evade host immunity and hijack cellular mechanisms to support proper virion formation and propagation. Some of these strategies encompass the manipulation of pathways involved in protein homeostasis, leading to changes in the host proteome and protein distribution within the cell. In this study, we performed a detailed analysis of the interplay between IAV and the host cells proteostasis mechanisms throughout the entire infectious cycle. We reveal that IAV infection induces the activation of the inositol requiring enzyme 1 (IRE1) branch of the unfolded protein response (UPR), at an infection stage that coincides with high rates of viral protein translation. This activation is particularly important for infection, as attenuation of virus production was observed upon IRE1 inhibition. Concomitantly to UPR activation, we observed the accumulation of virus-induced insoluble protein aggregates, which contain both viral and host proteins and are associated with a dysregulation of the host cell RNA metabolism. We demonstrate that this accumulation is important for IAV propagation, as its prevention using a quinoline-steroid hybrid compound significantly reduces the number of produced infectious virus particles. Our data suggests that the formation of these insoluble protein aggregates favors the final steps of the infection cycle, more specifically the virion assembly. Our findings reveal additional mechanisms by which IAV disrupts the host cell proteostasis to favor infection and uncover new cellular targets that can be explored for the development of host-directed antiviral strategies.

microbiology↗

bioRxiv2023

Westwards expansion of the European catfish Silurus glanis in the Douro River (Portugal)

The current study reports the first occurrence and the spread of the European catfish Silurus glanis (Family: Siluridae) in the Portuguese section of the Douro River, suggesting a potential expansion of its distribution in Portugal either via westward dispersal across international rivers and/or human-assisted introductions into new reservoirs and drainages. European catfish has unique features (e.g., opportunistic predator, hunting, and aggregation behaviour) that make it highly suitable for establishing self-sustaining populations in new areas and likely contribute to its invasion success. The species may severely affect native prey communities and modify food web structure and ecosystem functioning. Efficient and sustainable management actions are needed to prevent further introductions in the future.

ecology↗

bioRxiv2022

AdipoQ - a simple, open-source software to quantify adipocyte morphology and function in tissues and in vitro

The different adipose tissues can be distinguished according to their function. For example, white adipose tissue (WAT) stores energy in form of lipids, whereas brown adipose tissue (BAT) dissipates energy in the form of heat. These functional differences are represented in the respective adipocyte morphology: whereas white adipocytes contain large, unilocular lipid droplets, brown adipocytes contain smaller, multilocular lipid droplets. However, an automated, image-analysis pipeline to comprehensively analyze adipocytes in vitro in cell culture as well as ex vivo in tissue sections is missing. We here present AdipoQ, an open-source software implemented as ImageJ plugins that allows to analyze adipocytes in tissue sections and in vitro after histological and/or immunofluorescent labelling. AdipoQ is compatible with different imaging modalities and staining methods, allows batch processing of large datasets and simple post-hoc analysis, provides a broad band of parameters, and allows combining multiple fluorescent read-outs. Thereby, AdipoQ is of immediate use not only for basic research but also for clinical diagnosis.

cell biology↗

bioRxiv2022

Human cytomegalovirus vMIA inhibits MAVS oligomerization at peroxisomes in an MFF-dependent manner

Upon intracellular recognition of viral RNA, RIG-I-like proteins interact with MAVS at peroxisomes and mitochondria, inducing its oligomerization and the downstream production of direct antiviral effectors. The human cytomegalovirus (HCMV) is able to specifically evade this antiviral response, via its antiapoptotic protein vMIA. Besides suppressing the programmed cell death of infected cells, vMIA inhibits the antiviral signalling at mitochondria by inducing the organelles fragmentation, consequently hindering the interaction between MAVS and the endoplasmic reticulum protein STING. Here, we demonstrate that vMIA interferes with the peroxisomal antiviral signalling via a distinct mechanism that is independent of the organelles morphology and does not affect STING. vMIA interacts with MAVS at peroxisomes and inhibits its oligomerization, restraining downstream signalling, in an MFF-dependent manner. This study also demonstrates that vMIA is totally dependent on the organelles fission machinery to induce peroxisomal fragmentation, while this dependency is not observed at mitochondria. Furthermore, although we demonstrate that vMIA is also able to inhibit MAVS oligomerization at mitochondria, our results indicate that this process, such as the whole vMIA-mediated inhibition of the mitochondrial antiviral response, is independent of MFF. These observed differences in the mechanisms of action of vMIA towards both organelles, likely reflect their intrinsic differences and roles throughout the viral infection. This study uncovers specific molecular mechanisms that may be further explored as targets for antiviral therapy and highlights the relevance of peroxisomes as platforms for antiviral signalling against HCMV.

cell biology↗

bioRxiv2020

Cis-regulatory similarities in the zebrafish and human pancreas uncover potential disease-related enhancers

Introductory paragraphThe pancreas is a central organ for human diseases that have a dramatic societal burden, such as pancreatic cancer and diabetes1,2. Non-coding cis-regulatory elements (CREs) of DNA control gene expression3,4, being required for proper pancreas function. Most disease-associated alleles5,6 are non-coding, often overlapping with CREs5, suggesting that alterations in these regulatory sequences contribute to human pancreatic diseases by impairing gene expression. However, functional testing of CREs in vivo is not fully explored. Here we analysed histone modifications, transcription, chromatin accessibility and interactions, to identify zebrafish pancreas CREs and their human functional equivalents, uncovering disease-associated sequences across species. We found a human pancreatic enhancer whose deletion impairs the tumour suppressor gene ARID1A expression, conferring a potential tumour suppressor role to this non-coding sequence. Additionally, we identified a zebrafish ptf1a distal enhancer which deletion generates pancreatic agenesis, demonstrating the causality of this condition in humans7 and the interspecies functional equivalency of enhancers.

genomics↗

bioRxiv2020

Efficient phasing and imputation of low-coverage sequencing data using large reference panels

Low-coverage whole genome sequencing followed by imputation has been proposed as a cost-effective genotyping approach for disease and population genetics studies. However, its competitiveness against SNP arrays is undermined as current imputation methods are computationally expensive and unable to leverage large reference panels. Here, we describe a method, GLIMPSE, for phasing and imputation of low-coverage sequencing datasets from modern reference panels. We demonstrate its remarkable performance across different coverages and human populations. It achieves imputation of a full genome for less than $1, outperforming existing methods by orders of magnitude, with an increased accuracy of more than 20% at rare variants. We also show that 1x coverage enables effective association studies and is better suited than dense SNP arrays to access the impact of rare variations. Overall, this study demonstrates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.

bioinformatics↗

bioRxiv2017

In Vitro Study Of Dentin Hypersensitivity Treated By Whitlockite Glass-Ceramics

The aim of this study is to evaluate the potential of a bioactive glass based on the 3CaO.P2O5-SiO2MgO-system and its glassceramics containing whitlockite on the remineralization of dentin as a possible treatment to dentin hypersensitivity. For that, 40 third molar human teeth were artificially demineralized and randomly distributed in 4 groups (n = 10): G1 - Negative Control (no treatment), G2 - Positive Control (treated by Bioglass(R) 45S5), G3 - BG (treated by bioactive glass based on 3CaO.P2O5-SiO2-MgOsystem), and G4 - BGC (treated by bioactive whitlockite glass-ceramics). After treatment, the samples were emerged in artificial saliva and stored for 7 days in a controlled temperature of 37{o}C. After that, scanning electron microscopy (SEM) and atomic force microscopy (AFM) was used to evaluate samples morphology. The analysis confirmed the formation of hydroxyapatite on the surface of all the biomaterials studied, that in the dentine specimens treated by bioactive glass and whitlockite glas-ceramic most of the dentinal tubules were completely occluded.

bioengineering↗